RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zrJ8Mm/RM_1364306.ThuApr101846162025 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1744335975 Database = /dev/shm/rModeler.zrJ8Mm/GCF_028583425.1_MPM_Emac_v1.0 - Sequences = 76 - Bases = 2237397408 Storage Throughput = excellent ( 1777.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015700 bp ( 40015700 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:14 (hh:mm:ss) Elapsed Time Round Time: 00:14:39 (hh:mm:ss) Elapsed Time : 711 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19164 repeats masked totaling 3939552 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000300 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10000300 bp After Masking: 5953807 bp Masked: 40.46 % -- Input Database Coverage: 10000300 bp out of 2237397408 bp ( 0.45 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:44 (hh:mm:ss) Elapsed Time, 8150 HSPs Collected Number of families returned by RECON: 1438 Round Time: 00:03:27 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57865 repeats masked totaling 11976567 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015320 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30015320 bp After Masking: 17582353 bp Masked: 41.42 % -- Input Database Coverage: 40015620 bp out of 2237397408 bp ( 1.79 % ) Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:11:55 (hh:mm:ss) Elapsed Time, 55350 HSPs Collected Number of families returned by RECON: 4729 Round Time: 00:15:01 (hh:mm:ss) Elapsed Time : 144 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 191364 repeats masked totaling 39807627 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020459 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90020159 bp After Masking: 48957223 bp Masked: 45.62 % -- Input Database Coverage: 130036079 bp out of 2237397408 bp ( 5.81 % ) Sampling Time: 00:06:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:02:27 (hh:mm:ss) Elapsed Time, 232891 HSPs Collected Number of families returned by RECON: 12995 Round Time: 01:12:49 (hh:mm:ss) Elapsed Time : 502 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 636231 repeats masked totaling 131052260 bp(s). - TE Masking time 00:03:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017220 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 270016420 bp After Masking: 135307414 bp Masked: 49.89 % -- Input Database Coverage: 400053299 bp out of 2237397408 bp ( 17.88 % ) Sampling Time: 00:19:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 06:41:29 (hh:mm:ss) Elapsed Time, 638341 HSPs Collected Number of families returned by RECON: 40035 Round Time: 07:23:58 (hh:mm:ss) Elapsed Time : 1205 families discovered. RepeatScout/RECON discovery complete: 2580 families found Classification Time: 00:46:00 (hh:mm:ss) Elapsed Time Program Time: 09:55:54 (hh:mm:ss) Elapsed Time